Running CellProfiler with OMERO.blitz

This document shows how to run CellProfiler, an open source project to analyse and segment fluorescence microscopy images.

From the CellProfiler Website

CellProfiler cell image analysis software is designed for biologists without training in 
computer vision or programming to quantitatively measure phenotypes from thousands of 
images automatically. 

OMERO.cellprofiler supplies the OMEROJava connector and CellProfiler modules and subfunctions to download images from OMERO.blitz to CellProfiler and upload those images back to OMERO.blitz as a derived image of the original image.

Installing the OMERO.cellprofiler

To install the modules required by CellProfiler, to work with OMERO.blitz you need to download

• download CellProfiler source from CellProfiler.
• install wiki:OMEROJava
• copy the files from OMERO svn components/tools/cellprofiler
  • CPsubfunctions/CPOMEROimread.m
  • Modules/OMEROLoader.m
  • Modules/OMEROLoader.txt
  • Modules/UploadImages.m
• include the files in components/tools/OmeroM to your matlab path

The OMEROLoader Module

The OMEROLoader module specifies where CellProfiler should retrieve images from.

OMERO Specific

The OMEROLoader requires you to specify the path to the ice.config file, the dataset id to retrieve images from and username and password.

Image Related

The image is specified by the mapping between the name of the channel and the channel index.

UploadImages Module

The UploadImages Module uploads the segmented images into OMERO as a derived pixels of the original image.

Convert to Images

For the upload method to work correctly the convert to images module must specify that the images are saved as greyscale.